/usr/include/kmc/mmer.h is in libkmc-dev 2.3+dfsg-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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This file is a part of KMC software distributed under GNU GPL 3 licence.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
Version: 2.3.0
Date : 2015-08-21
*/
#ifndef _MMER_H
#define _MMER_H
#include "kmer_defs.h"
// *************************************************************************
// *************************************************************************
class CMmer
{
uint32 str;
uint32 mask;
uint32 current_val;
uint32* norm;
uint32 len;
static uint32 norm5[1 << 10];
static uint32 norm6[1 << 12];
static uint32 norm7[1 << 14];
static uint32 norm8[1 << 16];
static bool is_allowed(uint32 mmer, uint32 len)
{
if ((mmer & 0x3f) == 0x3f) // TTT suffix
return false;
if ((mmer & 0x3f) == 0x3b) // TGT suffix
return false;
if ((mmer & 0x3c) == 0x3c) // TG* suffix
return false;
for (uint32 j = 0; j < len - 3; ++j)
if ((mmer & 0xf) == 0) // AA inside
return false;
else
mmer >>= 2;
if (mmer == 0) // AAA prefix
return false;
if (mmer == 0x04) // ACA prefix
return false;
if ((mmer & 0xf) == 0) // *AA prefix
return false;
return true;
}
friend class CSignatureMapper;
struct _si
{
static uint32 get_rev(uint32 mmer, uint32 len)
{
uint32 rev = 0;
uint32 shift = len*2 - 2;
for(uint32 i = 0 ; i < len ; ++i)
{
rev += (3 - (mmer & 3)) << shift;
mmer >>= 2;
shift -= 2;
}
return rev;
}
static void init_norm(uint32* norm, uint32 len)
{
uint32 special = 1 << len * 2;
for(uint32 i = 0 ; i < special ; ++i)
{
uint32 rev = get_rev(i, len);
uint32 str_val = is_allowed(i, len) ? i : special;
uint32 rev_val = is_allowed(rev, len) ? rev : special;
norm[i] = MIN(str_val, rev_val);
}
}
_si()
{
init_norm(norm5, 5);
init_norm(norm6, 6);
init_norm(norm7, 7);
init_norm(norm8, 8);
}
}static _init;
public:
CMmer(uint32 _len);
inline void insert(uchar symb);
inline uint32 get() const;
inline bool operator==(const CMmer& x);
inline bool operator<(const CMmer& x);
inline void clear();
inline bool operator<=(const CMmer& x);
inline void set(const CMmer& x);
inline void insert(const char* seq);
};
//--------------------------------------------------------------------------
inline void CMmer::insert(uchar symb)
{
str <<= 2;
str += symb;
str &= mask;
current_val = norm[str];
}
//--------------------------------------------------------------------------
inline uint32 CMmer::get() const
{
return current_val;
}
//--------------------------------------------------------------------------
inline bool CMmer::operator==(const CMmer& x)
{
return current_val == x.current_val;
}
//--------------------------------------------------------------------------
inline bool CMmer::operator<(const CMmer& x)
{
return current_val < x.current_val;
}
//--------------------------------------------------------------------------
inline void CMmer::clear()
{
str = 0;
}
//--------------------------------------------------------------------------
inline bool CMmer::operator<=(const CMmer& x)
{
return current_val <= x.current_val;
}
//--------------------------------------------------------------------------
inline void CMmer::set(const CMmer& x)
{
str = x.str;
current_val = x.current_val;
}
//--------------------------------------------------------------------------
inline void CMmer::insert(const char* seq)
{
switch (len)
{
case 5:
str = (seq[0] << 8) + (seq[1] << 6) + (seq[2] << 4) + (seq[3] << 2) + (seq[4]);
break;
case 6:
str = (seq[0] << 10) + (seq[1] << 8) + (seq[2] << 6) + (seq[3] << 4) + (seq[4] << 2) + (seq[5]);
break;
case 7:
str = (seq[0] << 12) + (seq[1] << 10) + (seq[2] << 8) + (seq[3] << 6) + (seq[4] << 4 ) + (seq[5] << 2) + (seq[6]);
break;
case 8:
str = (seq[0] << 14) + (seq[1] << 12) + (seq[2] << 10) + (seq[3] << 8) + (seq[4] << 6) + (seq[5] << 4) + (seq[6] << 2) + (seq[7]);
break;
default:
break;
}
current_val = norm[str];
}
#endif
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